I have paired-end reads for a genome and a specific contig of interest. I would like to prolong my contig as much as possible using PRICE. I tried the following command line:
./PriceTI -fp L_raff_FAM23217_raw_reads_1.fq L_raff_FAM23217_raw_reads_2.fq 150 -icf contig.fasta 1 1 5 -o contig_extended.fasta -nc 5 -mpi 95
However, I obtained a very weird output file with additional contigs. Here is an example of an output file obtained after cycle 1:
>contig_1 (14073nt) TGTAATAGAGGGGGCTTTATCT... >contig_2 (340nt) TCATTATTGTCG... >contig_3 (307nt) CTCTTCGGGTTTTC...
I don't understand why there are additional contigs. I just want an extension of my original contig (initial size = 13 035 bp).
Is there a problem with my command line?
Thank you in advance for your help!